Preheat and prep the squash: Heat your oven to 400°F (200°C).
Halve the spaghetti squash lengthwise and scoop out the seeds. Drizzle cut sides with a little olive oil and season with salt and pepper. Place cut-side down on a lined baking sheet.
Roast the squash: Bake for 35–45 minutes, depending on size, until the skin yields slightly to pressure and strands pull easily with a fork.
If the strands feel watery, cook 5–10 minutes more.
Cool and shred: Let the squash cool for 5–10 minutes. Use a fork to scrape the flesh into strands. Transfer to a bowl and gently squeeze with paper towels or a clean kitchen towel to remove excess moisture. This step keeps the bake from getting soupy.
Brown the turkey: While the squash roasts, heat 1 tablespoon olive oil in a large skillet over medium heat.
Add the onion and cook 3–4 minutes until translucent. Stir in garlic and cook 30 seconds until fragrant. Add ground turkey, breaking it up with a spoon, and cook until no longer pink, about 5–7 minutes.
Season and sauce: Stir in Italian seasoning, red pepper flakes, 1/2 teaspoon salt, and black pepper.
Pour in the marinara and bring to a gentle simmer for 2–3 minutes to let the flavors blend. Taste and adjust seasoning.
Combine the base: In a large mixing bowl, combine the shredded spaghetti squash and the turkey marinara mixture. Mix gently until evenly coated.
Assemble the bake: Lightly grease a 9x13-inch baking dish.
Spread the squash-turkey mixture into an even layer. Top with mozzarella and sprinkle Parmesan over the top.
Bake: Reduce oven temperature to 375°F (190°C). Bake for 20–25 minutes, until the cheese is melted and bubbling.
For a golden top, broil for 2–3 minutes at the end, keeping a close eye on it.
Rest and garnish: Let the bake rest 5–10 minutes to set. Garnish with torn basil or chopped parsley. Serve warm.